comparison celesta.xml @ 2:41aaffbb9473 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/celesta commit ace07227a376d2684ec9afc37da91be789314635

1:44d4c885d9b5

                    --lowexpthresh '${runmode.options.low_thresholds_file}'
            #end if
            #if $runmode.options.high_thresholds_file:
                    --highexpthresh '${runmode.options.high_thresholds_file}'
            #end if  
            #for $p in $plot_cells:
                && Rscript '$__tool_directory__/celesta_plot_cells.R'
                    --prior '$prior_info'
                    --celltypes '${p.cell_types}'
                    --size '$p.test_size' 
                    --height '$p.height' 
                    --width '$p.width' 
                    --dpi '$p.dpi' 
            #end for
        #end if
        ]]>
    </command>
    <configfiles>

            <output name="assign_cells_output">
                <assert_contents>
                    <has_h5_keys keys="obs/celesta_final_cell_type" />
                </assert_contents>
            </output>
            <assert_stdout>
                <has_text text="vasculature 273" />
            </assert_stdout>
        </test>
        <test expect_num_outputs="3">
            <param name="anndata" value="celesta_image.h5ad" />
            <param name="prior_info" value="celesta_prior.csv" />
            <param name="filter" value="filter" />

            <output name="assign_cells_rds">
                <assert_contents>
                    <has_size value="1400000" delta="100000" />
                </assert_contents>
            </output>
            <assert_stdout>
                <has_text text="vasculature 168" />
            </assert_stdout>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

2:41aaffbb9473

                    --lowexpthresh '${runmode.options.low_thresholds_file}'
            #end if
            #if $runmode.options.high_thresholds_file:
                    --highexpthresh '${runmode.options.high_thresholds_file}'
            #end if  
            #for $p in $runmode.plot_cells:
                && Rscript '$__tool_directory__/celesta_plot_cells.R'
                    --prior '$prior_info'
                    --celltypes '${p.cell_types}'
                    --size '${p.test_size}' 
                    --height '${p.height}' 
                    --width '${p.width}' 
                    --dpi '${p.dpi}' 
            #end for
        #end if
        ]]>
    </command>
    <configfiles>

            <output name="assign_cells_output">
                <assert_contents>
                    <has_h5_keys keys="obs/celesta_final_cell_type" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="anndata" value="celesta_image.h5ad" />
            <param name="prior_info" value="celesta_prior.csv" />
            <param name="filter" value="filter" />

            <output name="assign_cells_rds">
                <assert_contents>
                    <has_size value="1400000" delta="100000" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**